The controversial 32-year-old, who said he was not initially designated as the penalty taker, stepped up in the 63rd minute of the Group Five match in Santiago and fired his shot past opposite number Diego Carranza.
"We had to score and I accepted the responsibility," Herrera told reporters as the Chilean side went top of the group with nine points from four games after completing a double over their Peruvian opponents.
Herrera, second-choice goalkeeper for the Chilean national side, was last year found guilty of killing a 22-year-old woman while speeding.
The prosecution had sought a three-year prison sentence, arguing that Herrera was driving under the influence of alcohol, but a judge ruled that he could go free.
In November, Herrera had to miss a friendly against Brazil in Toronto after being refused a Canadian visa.
Uruguay's Nacional were all but mathematically eliminated when they lost 1-0 at home to Atletico Nacional in Group Six after Edwin Cardona scored a breakaway goal in the second half for the Colombia visitors.
The 1971, 1980 and 1981 champions are bottom of the group with one point from four games.
An early goal by Juan Manuel Ferreyra gave Botafogo a 1-0 win over Independiente Jose Teran which took the Brazilians top of Group Two, although the Ecuadorean side created more chances.
A 27,000 crowd watched the match at Rio de Janeiro's Maracana stadium, roughly one third of its capacity.
Colombia's Santa Fe, semi-finalists last season, needed a late equaliser from Omar Perez, his second goal of the game, to force a 2-2 draw at home to Venezuelans Zamora, who came from behind to lead with a brace from Juan Manuel Falcon.
Both teams have four points in Group Four, three behind defending champions and leaders Atletico Mineiro.
Mexico's Santos Laguna extended their lead at the top of Group Eight with a comfortable 3-0 win over Deportivo Anzoategui of Venezuela.
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